Microarray data analysis on gene and miRNA expression to identify biomarkers in non-small cell lung cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32299382", "kind": "science-record", "revision": 7, "content_hash": "sha256:30b43667c1b64e1e3d2dff8d895f039d368a0697d5585214043c43d02eae66a4", "created_at": "2026-11-01T15:40:59Z", "updated_at": "2026-11-01T22:01:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Microarray data analysis on gene and miRNA expression to identify biomarkers in non-small cell lung cancer.", "doi": "10.1186/s12885-020-06829-x", "pmid": "32299382", "authors": ["Xiang Jin", "Yinghui Guan", "Zhen Zhang", "Hongyue Wang"], "journal": "BMC cancer", "year": 2020, "abstract": "BACKGROUND: The aim of this study was to gain further investigation of non-small cell lung cancer (NSCLC) tumorigenesis and identify biomarkers for clinical management of patients through comprehensive bioinformatics analysis.\nMETHODS: miRNA and mRNA microarray datasets were downloaded from GEO (Gene Expression Omnibus) database under the accession number GSE102286 and GSE101929, respectively. Genes and miRNAs with differential expression were identified in NSCLC samples compared with controls, respectively. The interaction between differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRs) was predicted, followed by functional enrichment analysis, and construction of miRNA-gene regulatory network, protein-protein interaction (PPI) network, and competing endogenous RNA (ceRNA) network. Through comprehensive bioinformatics analysis, we anticipate to find novel therapeutic targets and biomarkers for NSCLC.\nRESULTS: A total of 123 DEmiRs (5 up- and 118 down-regulated miRNAs) and 924 DEGs (309 up- and 615 down-regulated genes) were identified. These genes and miRNAs were significantly involved in different pathways including adherens junction, relaxin signaling pathway, and axon guidance. Furthermore, hsa-miR-9-5p, has-miR-196a-5p and hsa-miR-31-5p, as well as hsa-miR-1, hsa-miR-218-5p and hsa-miR-135a-5p were shown to have higher degree in the miRNA-gene regulatory network and ceRNA network, respectively. Furthermore, BIRC5 and FGF2, as well as RTKN2 and SLIT3 were hubs in the PPI network and ceRNA network, respectively.\nCONCLUSION: Several pathways (adherens junction, relaxin signaling pathway, and axon guidance) miRNAs (hsa-miR-9-5p, has-miR-196a-5p, hsa-miR-31-5p, hsa-miR-1, hsa-miR-218-5p and hsa-miR-135a-5p) and genes (BIRC5, FGF2, RTKN2 and SLIT3) may play important roles in the pathogenesis of NSCLC.", "claims": [{"id": "claim-method", "statement": "Non-paired t-test provided by limma [15] were used to calculate the P-values of significant gene expression differences.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32299382", "locator": "sections[4] \"Data preprocessing and DEmiRs and DEGs screening\" paragraph 4", "quote": "Non-paired t-test provided by limma [15] were used to calculate the P-values of significant gene expression differences."}], "state": "complete"}, {"id": "claim-data-access", "statement": "In this study, miRNA and mRNA microarray datasets were downloaded from the GEO database under the accession number GSE102286 and GSE101929, respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32299382", "locator": "sections[3] \"Source of the microarray data\" paragraph 2", "quote": "In this study, miRNA and mRNA microarray datasets were downloaded from the GEO database under the accession number GSE102286 and GSE101929, respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:32299382"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE101929"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE101929"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32299382", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12885-020-06829-x", "sha256": 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"section_index": 12, "section_title": "Functional enrichment analysis of DEmiRs and DEGs", "row_count": 67, "column_count": 5}, "table": {"label": "Table 1", "caption": "The enriched pathways by differentially expressed miRNAs", "rows": [["miRNA", "ID", "Pathway", "P value", "Count"], ["hsa-miR-9-5p", "hsa04933", "AGE-RAGE signaling pathway in diabetic complications", "4.84E-05", "4"], ["hsa04926", "Relaxin signaling pathway", "2.51E-03", "3"], ["hsa04218", "Cellular senescence", "4.51E-03", "3"], ["hsa04115", "p53 signaling pathway", "9.18E-03", "2"], ["hsa04520", "Adherens junction", "1.03E-02", "2"], ["hsa04350", "TGF-beta signaling pathway", "1.38E-02", "2"], ["hsa04974", "Protein digestion and absorption", "1.57E-02", "2"], ["hsa05146", "Amoebiasis", "1.77E-02", "2"], ["hsa05142", "Chagas disease (American trypanosomiasis)", "1.99E-02", "2"], ["hsa-miR-31-3p", "hsa04520", "Adherens junction", "1.90E-03", "2"], ["hsa04360", "Axon guidance", "1.08E-02", "2"], ["hsa05165", "Human 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"4"], ["hsa04520", "Adherens junction", "6.35E-04", "4"], ["hsa05202", "Transcriptional misregulation in cancer", "3.41E-03", "5"], ["hsa00910", "Nitrogen metabolism", "3.86E-03", "2"], ["hsa00601", "Glycosphingolipid biosynthesis - lacto and neolacto series", "9.62E-03", "2"], ["hsa04666", "Fc gamma R-mediated phagocytosis", "1.37E-02", "3"], ["hsa-miR-130a-3p", "hsa04261", "Adrenergic signaling in cardiomyocytes", "1.47E-03", "4"], ["hsa04911", "Insulin secretion", "3.14E-03", "3"], ["hsa04015", "Rap1 signaling pathway", "5.38E-03", "4"], ["hsa04960", "Aldosterone-regulated sodium reabsorption", "7.33E-03", "2"], ["hsa04926", "Relaxin signaling pathway", "1.02E-02", "3"], ["hsa04961", "Endocrine and other factor-regulated calcium reabsorption", "1.16E-02", "2"], ["hsa-miR-1246", "hsa04925", "Aldosterone synthesis and secretion", "8.59E-04", "3"], ["hsa04022", "cGMP-PKG signaling pathway", "3.92E-03", "3"], ["hsa04927", "Cortisol synthesis and secretion", "6.97E-03", "2"], ["hsa04918", "Thyroid hormone synthesis", "9.52E-03", "2"], ["hsa04911", "Insulin secretion", "1.24E-02", "2"], ["hsa04922", "Glucagon signaling pathway", "1.79E-02", "2"], ["hsa04928", "Parathyroid hormone synthesis, secretion and action", "1.89E-02", "2"], ["hsa04725", "Cholinergic synapse", "2.09E-02", "2"], ["hsa04724", "Glutamatergic synapse", "2.17E-02", "2"], ["hsa04926", "Relaxin signaling pathway", "2.77E-02", "2"], ["hsa04728", "Dopaminergic synapse", "2.81E-02", "2"], ["hsa04915", "Estrogen signaling pathway", "3.05E-02", "2"], ["hsa04151", "PI3K-Akt signaling pathway", "3.17E-02", "3"], ["hsa04261", "Adrenergic signaling in cardiomyocytes", "3.34E-02", "2"], ["hsa04310", "Wnt signaling pathway", "3.43E-02", "2"], ["hsa04934", "Cushing’s syndrome", "3.78E-02", "2"], ["hsa-miR-1", "hsa05030", "Cocaine addiction", "2.45E-04", "3"], ["hsa04668", "TNF signaling pathway", "2.47E-03", "3"], ["hsa05034", "Alcoholism", "1.03E-02", "3"], ["hsa05031", "Amphetamine addiction", 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